Okay, new issue. I will setup a series of images to be “windows” over layed on my video. After I first put them in, later on I will try to “stretch” them, so they take up a different amount of time on my video. But for some reason, when I stretch them longer than when I first laid them down, they lose all filter effects.
For example, here’s minute 2:49. Everything looks great.

Your filters on Office.jpg are not “lost;” they are simply trimmed. “Trim” refers to a starting and/or ending time different than the clip. Filters can be trimmed in the Keyframes panel. When you change the duration of a clip, Shotcut is supposed to adjust the start/end of all non-trimmed filters. It is possible you accidentally trimmed them, but it sounds like perhaps not. It is possible Shotcut has a bug in properly detecting trimmed or not in certain scenarios, for example, when there is a transition involved. I will look into that. In the meantime, you can fix this in the Keyframes panel for each affected filter of each affected clip and drag the red right edge to the right.

However, this does not fix it for the transition to the next image. So, it appears the bug occurs when you add the filters, make the transition, and then adjust the duration of the image clip. I will try to reproduce it.